The weekend's events come just two weeks after a series of seven fires in the same region killed 24 horses.
The emergency services were called to a farm in Payerne at around 1.10am on Saturday morning, Vaud police said in a statement.
Eleven cows were saved, but around a dozen died, plus several calves. Their owners were successfully evacuated and no person was injured.
Less than an hour later a police patrol spotted another fire on an isolated farm building between Domdidier and Dompierre, Fribourg police said.
Police and the fire service attended the scene, and were able to free a number of cows from the barn. However a number suffered serious burns and had to be put down.
A police spokesman told news agency ATS that of the 108 cows at the farm, 36 died.
Those that were freed and ran off were later recuperated by the farmer, he added.
Currently the cause of the fires is unknown, both police forces said.
No link has been established between the two fires.
Two weeks ago, also in the early hours of the morning, a series of seven fires broke out in the same region, including one at the National Equestrian Centre in Avenches, where more than 20 horses died.
Police said those fires were criminal acts, and later arrested a suspect.